rs7543182

Positions:

• chr1-70874290-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000370931.7(PTGER3):​c.*24-21431G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,040 control chromosomes in the GnomAD database, including 3,441 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3441 hom., cov: 32)
• Consequence: PTGER3 ENST00000370931.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

Genes affected

PTGER3 (HGNC:9595): (prostaglandin E receptor 3) The protein encoded by this gene is a member of the G-protein coupled receptor family. This protein is one of four receptors identified for prostaglandin E2 (PGE2). This receptor may have many biological functions, which involve digestion, nervous system, kidney reabsorption, and uterine contraction activities. Studies of the mouse counterpart suggest that this receptor may also mediate adrenocorticotropic hormone response as well as fever generation in response to exogenous and endogenous stimuli. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198714.2	c.*24-21431G>T		intron_variant
PTGER3	NM_198716.2	c.1105-21431G>T		intron_variant
PTGER3	NM_198717.2	c.1078-21431G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000370931.7	c.*24-21431G>T		intron_variant		1		A1
PTGER3	ENST00000460330.5	c.1105-21431G>T		intron_variant		1		A2
PTGER3	ENST00000628037.2	c.1078-21431G>T		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28357 AN: 151922 Hom.: 3436 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.192

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.187 AC: 28360 AN: 152040 Hom.: 3441 Cov.: 32 AF XY: 0.186 AC XY: 13835 AN XY: 74318

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.192

Alfa AF: 0.224 Hom.: 5264

Bravo AF: 0.198

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.39
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7543182; hg19: chr1-71339973;